Clarke only managed a seventh-place finish in his heat to crash out of the competition, coming home in a time of 13.53s.
"I knew this race was a do-or-die race. The first five was the fastest five I've ever done but by the end I was just too tired," he told BBC Sport.
"I came fourth in the Olympics but God they're quick. It's a year to go to the Olympics and that's what I've been dreaming of. If I can hang on to my fitness I will get there."
World record holder Aries Merritt also made the final, just five days before undergoing a kidney transplant.